<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<!-- DTD for polymer definitions, used by the
'massXpert' mass spectrometry application.
Copyright 2006,2007,2008 Filippo Rusconi
Licensed under the GNU GPL -->
<!DOCTYPE polchemdefinition [
<!ELEMENT polchemdefinition (polchemdefdata)>
<!ATTLIST polchemdefinition version NMTOKEN #REQUIRED>
<!ELEMENT polchemdefdata (name , leftcap , rightcap , codelen , ionizerule , monomers , modifs , crosslinkers , cleavageagents , fragmentationpathways)>
<!ELEMENT ionizerule (formula , charge , level)>
<!ELEMENT monomers (mnm)*>
<!ELEMENT modifs (mdf)*>
<!ELEMENT crosslinkers (clk)*>
<!ELEMENT cleavageagents (cla)*>
<!ELEMENT fragmentationpathways (fgp)*>
<!ELEMENT mnm (name , code , formula)>
<!ELEMENT mdf (name , formula , targets , maxcount)>
<!ELEMENT clk (name , formula , modifname*)>
<!ELEMENT cla (name , pattern , clr*)>
<!ELEMENT fgp (name , end , formula , sidechaincontrib , comment? , fgr*)>
<!ELEMENT clr (name , (le-mnm-code , le-formula)? , (re-mnm-code , re-formula)?)>
<!ELEMENT fgr (name , formula , prev-mnm-code? , curr-mnm-code? , next-mnm-code? , comment?)>
<!ELEMENT leftcap (#PCDATA)>
<!ELEMENT rightcap (#PCDATA)>
<!ELEMENT codelen (#PCDATA)>
<!ELEMENT charge (#PCDATA)>
<!ELEMENT maxcount (#PCDATA)>
<!ELEMENT level (#PCDATA)>
<!ELEMENT name (#PCDATA)>
<!ELEMENT modifname (#PCDATA)>
<!ELEMENT code (#PCDATA)>
<!ELEMENT formula (#PCDATA)>
<!ELEMENT sidechaincontrib (#PCDATA)>
<!ELEMENT targets (#PCDATA)>
<!ELEMENT pattern (#PCDATA)>
<!ELEMENT end (#PCDATA)>
<!ELEMENT le-mnm-code (#PCDATA)>
<!ELEMENT re-mnm-code (#PCDATA)>
<!ELEMENT le-formula (#PCDATA)>
<!ELEMENT re-formula (#PCDATA)>
<!ELEMENT comment (#PCDATA)>
<!ELEMENT prev-mnm-code (#PCDATA)>
<!ELEMENT curr-mnm-code (#PCDATA)>
<!ELEMENT next-mnm-code (#PCDATA)>
]>
<polchemdefinition version="2">
	<polchemdefdata>
		<name>nucac</name>
		<leftcap>+OH</leftcap>
		<rightcap>+H</rightcap>
		<codelen>3</codelen>
		<ionizerule>
			<formula>-H</formula>
			<charge>1</charge>
			<level>1</level>
		</ionizerule>
		<monomers>
			<mnm>
				<name>Dadenine</name>
				<code>Da</code>
				<formula>C10H12O5N5P</formula>
			</mnm>
			<mnm>
				<name>Dguanine</name>
				<code>Dg</code>
				<formula>C10H12O6N5P</formula>
			</mnm>
			<mnm>
				<name>Dthymine</name>
				<code>Dt</code>
				<formula>C10H13O7N2P</formula>
			</mnm>
			<mnm>
				<name>Dcytosine</name>
				<code>Dc</code>
				<formula>C9H12O6N3P1</formula>
			</mnm>
			<mnm>
				<name>PS-Dadenine</name>
				<code>Sda</code>
				<formula>C10H12O4SN5P</formula>
			</mnm>
			<mnm>
				<name>PS-Dguanine</name>
				<code>Sdg</code>
				<formula>C10H12O5SN5P</formula>
			</mnm>
			<mnm>
				<name>PS-Dthymine</name>
				<code>Sdt</code>
				<formula>C10H13O6SN2P</formula>
			</mnm>
			<mnm>
				<name>PS-Dcytosine</name>
				<code>Sdc</code>
				<formula>C9H12O5SN3P1</formula>
			</mnm>
			<mnm>
				<name>Radenine</name>
				<code>Ra</code>
				<formula>C10H12O6N5P</formula>
			</mnm>
			<mnm>
				<name>Rguanine</name>
				<code>Rg</code>
				<formula>C10H12O7N5P</formula>
			</mnm>
			<mnm>
				<name>Rcytosine</name>
				<code>Rc</code>
				<formula>C9H12O7N3P1</formula>
			</mnm>
			<mnm>
				<name>Ruracile</name>
				<code>Ru</code>
				<formula>C9H11O8N2P</formula>
			</mnm>
			<mnm>
				<name>PS-Radenine</name>
				<code>Sra</code>
				<formula>C10H12O5SN5P</formula>
			</mnm>
			<mnm>
				<name>PS-Rguanine</name>
				<code>Srg</code>
				<formula>C10H12O6SN5P</formula>
			</mnm>
			<mnm>
				<name>PS-Rcytosine</name>
				<code>Src</code>
				<formula>C9H12O6SN3P1</formula>
			</mnm>
			<mnm>
				<name>PS-Ruracile</name>
				<code>Sru</code>
				<formula>C9H11O7SN2P</formula>
			</mnm>
		</monomers>
		<modifs>
			<mdf>
				<name>Dephosphorylate</name>
				<formula>-HPO3</formula>
				<targets>*</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Phosphorothioate</name>
				<formula>-O+S</formula>
				<targets>*</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Hairpin-cytosine</name>
				<formula>-H+C8H17O4+C23H32N5O5S</formula>
				<targets>*</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Oxidation</name>
				<formula>+O</formula>
				<targets>;Dg;Rg</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Phosphorylation</name>
				<formula>-H+H2PO3</formula>
				<targets>!</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>DiPhosphorylation</name>
				<formula>-H+H3P2O6</formula>
				<targets>!</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Methylation</name>
				<formula>-H+CH2</formula>
				<targets>;Dc;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>BiotLink</name>
				<formula>-H+C25H36N5O5S</formula>
				<targets>!</targets>
				<maxcount>1</maxcount>
			</mdf>
		</modifs>
		<crosslinkers>
			<clk>
				<name>Thymine-dimer</name>
				<formula>+H1-H1</formula>
			</clk>
		</crosslinkers>
		<cleavageagents>
			<cla>
				<name>EcoRI</name>
				<pattern>Dg/DaDaDtDtDc</pattern>
			</cla>
			<cla>
				<name>HindIII</name>
				<pattern>Da/DaDgDcDtDt</pattern>
			</cla>
			<cla>
				<name>SacI</name>
				<pattern>DgDaDgDcDt/Dc</pattern>
			</cla>
			<cla>
				<name>XhoI</name>
				<pattern>Dc/DtDcDgDaDgDg</pattern>
			</cla>
		</cleavageagents>
		<fragmentationpathways>
			<fgp>
				<name>a</name>
				<end>LE</end>
				<formula>-OH</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>a-B</name>
				<end>LE</end>
				<formula>-HOH+C5H8O5P</formula>
				<sidechaincontrib>-1</sidechaincontrib>
				<comment>abasic a fragment</comment>
			</fgp>
			<fgp>
				<name>b</name>
				<end>LE</end>
				<formula>+H</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>c</name>
				<end>LE</end>
				<formula>+PO2</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>d</name>
				<end>LE</end>
				<formula>+HPO3+H</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>w</name>
				<end>RE</end>
				<formula>+OH</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>x</name>
				<end>RE</end>
				<formula>-H</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>y</name>
				<end>RE</end>
				<formula>-HPO2+H</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>z</name>
				<end>RE</end>
				<formula>-HPO3-H</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
		</fragmentationpathways>
	</polchemdefdata>
</polchemdefinition>
